[gmx-users] Topology file error for a ligand
Anirban Ghosh
reach.anirban.ghosh at gmail.com
Mon Nov 23 13:55:08 CET 2009
Thanks a lot Mark and Justin for your replies.
If PRODRG results have to be taken with a pinch of salt, then can you please
suggest me how to get the proper topology for my ligand, just hints. In
particular the .itp file is missing the HZ, HB2 and HB3 hydrogen atoms,
which are present in the PDB and GRO files. But the other hydrogen atoms are
defined properly. Any suggestion is welcome.
Regards,
Anirban
On Mon, Nov 23, 2009 at 5:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Anirban Ghosh wrote:
>
>> Hi ALL,
>>
>> I want to do a simulation of a protein in presence of a ligand (L-DOPA). I
>> am trying to obtain the topology of L-DOPA from the PRODRG server. However I
>> am getting an error in the number of atoms in the PDB file (with all
>> hydrogens) and the topology parameter file. The PDB file consists of 25
>> atoms, but the itp file gives definition for 22 atoms (3 hydrogens are
>> missing). So every time there is an error w.r.t. number of atoms mismatch.
>>
>
> This is happening because PRODRG gives GROMOS-compatible topologies. They
> are united-atom. So naturally, if you attempt to use an all-atom structure,
> there will be mismatch.
>
> I also would not trust the PRODRG topology at face value, as I have posted
> across this list dozens of times.
>
> -Justin
>
>
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------
>> PDB:
>>
>> TITLE Gnomes, ROck Monsters And Chili Sauce
>> MODEL 1
>> ATOM 1 N DAH 1 15.600 17.820 -3.200 1.00 0.00
>> ATOM 2 CA DAH 1 16.490 17.500 -2.040 1.00 0.00
>> ATOM 3 C DAH 1 18.010 17.580 -2.400 1.00 0.00
>> ATOM 4 O DAH 1 18.560 16.790 -3.210 1.00 0.00
>> ATOM 5 CB DAH 1 16.100 16.180 -1.290 1.00 0.00
>> ATOM 6 CG DAH 1 14.980 16.190 -0.220 1.00 0.00
>> ATOM 7 CD1 DAH 1 13.790 16.990 -0.410 1.00 0.00
>> ATOM 8 CD2 DAH 1 15.130 15.410 0.970 1.00 0.00
>> ATOM 9 CE1 DAH 1 12.770 16.990 0.570 1.00 0.00
>> ATOM 10 CE2 DAH 1 14.100 15.400 1.950 1.00 0.00
>> ATOM 11 CZ DAH 1 12.900 16.200 1.750 1.00 0.00
>> ATOM 12 OE2 DAH 1 14.280 14.630 3.070 1.00 0.00
>> ATOM 13 OZ DAH 1 11.880 16.230 2.690 1.00 0.00
>> ATOM 14 OXT DAH 1 18.680 18.630 -1.760 1.00 0.00
>> ATOM 15 HA DAH 1 16.330 18.300 -1.320 1.00 0.00
>> ATOM 16 HB2 DAH 1 15.790 15.470 -2.050 1.00 0.00
>> ATOM 17 HB3 DAH 1 17.000 15.790 -0.820 1.00 0.00
>> ATOM 18 HD2 DAH 1 16.020 14.820 1.110 1.00 0.00
>> ATOM 19 HE1 DAH 1 11.880 17.580 0.420 1.00 0.00
>> ATOM 20 HD1 DAH 1 13.670 17.590 -1.300 1.00 0.00
>> ATOM 21 HE2 DAH 1 15.190 14.330 3.110 1.00 0.00
>> ATOM 22 HZ DAH 1 11.550 15.340 2.820 1.00 0.00
>> ATOM 23 H1 DAH 1 15.920 18.680 -3.630 1.00 0.00
>> ATOM 24 H2 DAH 1 15.640 17.070 -3.880 1.00 0.00
>> ATOM 25 H3 DAH 1 14.650 17.930 -2.880 1.00 0.00
>> TER
>> ENDMDL
>>
>> TOPOLOGY FILE:
>>
>> [ moleculetype ]
>> ; Name nrexcl
>> DAH 3
>>
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass
>> 1 OM 1 DAH O 1 -0.715 15.9994 2
>> C 1 DAH C 1 0.387 12.0110 3 OM 1 DAH
>> OXT 1 -0.716 15.9994 4 CH1 1 DAH CA 1
>> 0.178 13.0190 5 NL 1 DAH N 1 0.683 14.0067
>> 6 H 1 DAH H2 1 0.010 1.0080 7
>> H 1 DAH H3 1 0.010 1.0080 8 H 1 DAH
>> H1 1 0.011 1.0080 9 CH2 1 DAH CB 1
>> 0.152 14.0270 10 C 1 DAH CG 2 -0.020 12.0110
>> 11 CR1 1 DAH CD2 2 0.001 12.0110 12
>> HC 1 DAH HD2 2 0.019 1.0080 13 C 1 DAH
>> CE2 3 0.130 12.0110 14 OA 1 DAH OE2 3
>> -0.197 15.9994 15 H 1 DAH HE2 3 0.051 1.0080
>> 16 C 1 DAH CZ 3 0.130 12.0110 17
>> OA 1 DAH OZ 3 -0.197 15.9994 18 H 1 DAH
>> HZ 3 0.051 1.0080 19 CR1 1 DAH CE1 3
>> 0.001 12.0110 20 HC 1 DAH HE1 3 0.031 1.0080
>> 21 CR1 1 DAH CD1 4 0.000 12.0110 22
>> HC 1 DAH HD1 4 0.000 1.0080
>> [ bonds ]...
>>
>> -----------------------------------------------------------------------------------------------------------------------------------------------------------
>> How can I rectify this issue? Any suggestion is welcome. Thanks a lot.
>>
>> Regards,
>>
>> Anirban
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
> --
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